Structural Genomics @CNAG · CRG

We have contributed to the following books:


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Bibliography last updated on: 2023-11-23

There are 138 publications of article type

138.-Sandoval-Velasco, M.,  Dudchenko, O.,  Rodríguez, J.A.,  Pérez Estrada, C.,  Dehasque, M.,  Fontsere, C.,  Mak, S.S.T.,  Plotnikov, V.,  Khan, R.,  Weisz, D.,   Contessoto, V.G.,  Oliveira Junior, A.B.,  Kalluchi, A.,  Omer, A.D.,  Batra, S.B.,  Shamim, M.S.,  Durand, N.C.,  OConnell, B.,  Roca, A.L.,  Gnirke, A.,  Garcia-Treviño, I.,  Coke, R.,  Flanagan,J.P.,  Pletch, K.,  Ruiz-Herrera, A.,  Lander, E.S.,  Rowley, M.J.,  Onuchic, J.N.,  Dalén, L.,  Marti-Renom, M.A.,  Gilbert, M.T.P and Lieberman Aiden, E.
"Three-dimensional genome architecture persists in a 52,000-year-old woolly mammoth skin sample"
BioRxiv (2023) preprint   
137.-Kocanova, S.,  Raynal, F.,  Goiffon, I.,  Oksuz, B.A.,  Baù, D.,  Kamgoué, A.,  Cantaloube, S.,  Zhan, Y.,  Lajoie, B.,  Marti-Renom, M.A.,  Dekker, J. and Bystricky, K.
"Enhancer-driven local 3D chromatin domain folding modulates transcription in human mammary tumor cells"
Life Science Alliance (2023) 7 (2) e202302154  
Journal NCBI Related
136.-Yeh, SH.,  Strilets, T.,  Tan, W-L.,   Castillo, D.,   Medkour, H.,  Rey-Cadilhac, F.,  Serrato-Pomar, I.M.,   Rachenne, F.,  Chowdhury, A.,  Chuo, V.,  Azar, S.R.,  Singh, M.K.,  Hamel, M.,  Missé, D.,  Kini, R.M.,  Kenney, L.J.,  Vasilakis, N.,  Marti-Renom, M.A.,  Nir, G.,  Pompon, J. and Garcia-Blanco, M.A.
"The anti-immune dengue subgenomic flaviviral RNA is present in vesicles in mosquito saliva and is associated with increased infectivity"
PLOS Pathogens (2023) 19(3) e1011224  
Journal NCBI Related
135.-Mota-Gómez, I.,  Rodriguez, J.A.,  Dupont, S.,  Lao, O.,  Jedamzick, J.,  Kuhn, R.,  Lacadie, S.,   García-Moreno, S.A.,  Hurtado, A. Acemel, R.D.,  Capel, B.,  Marti-Renom, M.A. and Lupiáñez, D.G.
"Sex-determining 3D regulatory hubs revealed by genome spatial auto-correlation analysis"
BioRxiv (2022) preprint   
134.-Serna-Pujol, N.,  Salinas-Pena, M.S.,  Mugianesi, F.,  Le Dily, F.,  Marti-Renom, M.A. and Jordan, A.
"Coordinated changes in gene expression, H1 variant distribution and genome 3D conformation in response to H1 depletion"
Nucleic Acids Research (2022) 50 (7) 3892–3910  
Journal NCBI Related BioRxiv
133.-Álvarez-González, L.,  Arias-Sardá, C.,  Montes-Espuña, L.,  Marín-Gual, L.,  Vara, C.,  Lister, N.C.,  Cuartero, Y.,  Garcia, F.,  Deakin, J.,  Renfree, M.,  Robinson, T.J.,  Marti-Renom, M.A.,  Waters, P.D.,  Farré, M. and Ruiz-Herrera, A.
"Principles of 3D chromosome folding and evolutionary genome reshuffling in mammals"
Cell Reports (2022) 41(12) 111839  
132.-Galan, S.,  Serra, F. and Marti-Renom, M.A.
"Identification of chromatin loops from Hi-C interaction matrices by CTCF-CTCF topology classification"
NAR Genomics and Bioinformatics (2022) 4(1) lqac021.  
Journal NCBI Related BioRxiv
131.-Vilarrasa-Blasi, R.,  Verdaguer-Dot, N.,  Belver, L.,  Soler-Vila, P.,  Beekman, R.,  Chapaprieta, V.,  Kulis, M.,  Queirós, A.C.,  Parra, M.,  Calasanz, M.J.,  Agirre, X.,  Prosper, F.,  Beà, S.,  Colomer, D.,  Marti-Renom, M.A.,  Ferrando, A.,  Campo, E. and Martin-Subero, J.I.
"Insights into the mechanisms underlying aberrant SOX11 oncogene expression in mantle cell lymphoma"
Leukemia (2022) 36(2) 583-587  
Journal NCBI Related
130.-Mas, G.,  Santoro, F.,  Blanco, E.,  Gamarra Figueroa, G.,  Le Dily, F.,  Frigè, G,  Vidal, E.,  Mugianesi, F.,  Ballaré, C.,  Gutierrez, A.,  Sparavier, A.,  Marti-Renom, M.A.,  Minucci, S. and Di Croce, L.
"In vivo temporal resolution of acute promyelocytic leukemia progression reveals a role of Klf4 in suppressing early leukemic transformation"
Genes & Development (2022) 36 451-467  
Journal NCBI Related
129.-Di Stefano, M.,  Paulsen, J.,  Jost, D. and Marti-Renom, M.A.
"4D nucleome modeling"
Current Opinion in Genetics & Development (2021) 67 25-32  
Journal NCBI Related
128.-Gines, L.R.,  Lapi, E.,  Pancaldi, V.,  Cuenca, M.,  Castillo de Santa Pau, E.,  Madrid, M.,  Neyret-Kahn, H.,  Radvanyi, F.,   Rodriguez, J.A.,  Cuartero, Y.,  Serra, F.,  Le Dily, F.,  Valencia, A.,  Marti-Renom, M.A. and Real, F.X.
"STAG2 loss-of-function affects short-range genomic contacts and modulates urothelial differentiation in bladder cancer cells"
Nucleic Acids Research (2021) 49 (19) 11005–11021  
Journal NCBI Related BioRxiv
127.-Di Stefano, M.,  Nuetzmann, H-W.,  Marti-Renom, M.A. and Jost, D.
"Polymer modelling unveils the roles of heterochromatin and nucleolar organizing regions in shaping 3D genome organization in Arabidopsis thaliana"
Nucleic Acids Research (2021) 4 1840–1858  
Journal NCBI Related
126.-Mendieta-Esteban, J.,  Di Stefano, M.,  Castillo, D.,  Farabella, I. and Marti-Renom, M.A.
"3D reconstruction of genomic regions from sparse interaction data"
NAR Genomics and Bioinformatics (2021) 3(1) lqab017  
Journal NCBI Related BioRxiv
125.-Farabella, I.,  Di Stefano, M.,  Soler-Vila, P.,  Marti-Marimon, M. and Marti-Renom, M.A.
"Three-dimensional genome organization via triplex forming RNAs"
Nature Structural and Molecular Biology (2021) 28(11) 945-954  
Journal NCBI Related
124.-Di Stefano, M.,  Castillo, D.,  Serra, F.,  Farabella, I.,  Goodstadt, M. and Marti-Renom, M.A.
"Analysis, Modeling, and Visualization of Chromosome Conformation Capture Experiments."
Methods Mol Biol (2021) 2157 35-63  
Journal NCBI Related
123.-Marti-Renom, M.A.
"Benchmarking experiments with polymer modeling."
Nature Methods (2021) 18 456-457  
Journal NCBI Related
122.-Lopez de Maturana, E.,  Rodriguez, J.A.,  .../...,  Marti-Renom, M.A.,  Real, F.X. and Malats, N.
"A multilayered post-GWAS assessment on genetic susceptibility to pancreatic cancer"
Genome Medicine (2021) 13(1) 15  
Journal NCBI Related BioRxiv
121.-Vilarrasa-Blasi, R.,  Soler-Vila, P.,  Verdaguer-Dot, N.,  Russinol, N.,  Di Stefano, M.,  Chapaprieta, V.,  Clot, G.,  Farabella, I.,  Cusco, P.,  Agirre, X.,  Prosper, F.,  Beekman, R.,  Bea, S.,  Colomer, D.,  Gut, I.,  Stunnenberg, H.,  Campo, E.,  Marti-Renom, M.A. and Martin-Subero, J.I.
"Dynamics of genome architecture and chromatin function during human B cell differentiation and neoplastic transformation"
Nature Communications (2021) 12(1) 651-667  
Journal NCBI Related BioRxiv
120.-Vara,C.,  Paytuví-Gallart, A.,  Cuartero, Y,,  Álvarez-González, A.,  Garcia, F.,  Florit-Sabater, B.,  Marín-Gual, L.,  Capilla, L.,  Albert-Lizandra, A.,  Sanchéz-Guillén, R.A.,  Sarrate, Z.,  Cigliano, R.A.,  Sanseverino, W.,  Ventura, J.,  Marti-Renom, M.A.,  Le Dily, F. and Ruiz-Herrera, A.
"The Impact of Chromosomal Fusions on 3D Genome Folding and Recombination in the Germ Line"
Nature Communications (2021) 12 2981   
Journal NCBI Related
119.-Sandoval-Velasco, M.,  Rodriguez, J.A.,  Perez-Estrada, C.,  Zhang, G.,  Lieberman-Aiden, E.,  Marti-Renom, M.A.,  Gilbert, M.T.P and Smith, O
"Hi-C chromosome conformation capture sequencing of avian genomes using the BGISEQ-500 platform"
GigaScience (2020) 9(8) giaa087  
Journal NCBI Related
118.-Sati, S.,  Bonev, B.,  Szabo, Q.,   Jost, D.,  Bensadoun, P.,  Serra, F.,   Loubiere, V.,   Papadopoulos, G.L.,  Rivera-Mulia, J.C.,  Fritsch, L.,  Bouret, P.,  Castillo, D.,   Gelpi, J.LL.,  Orozco, M.,  Vaillant, C.,  Pellestor, F.,  Bantignies, F.,  Marti-Renom, M.A.,  Gilbert, D.,  Lemaitre, J.L. and Cavalli, G.
"4D genome rewiring during oncogene induced and replicative senescence"
Molecular Cell (2020) 78 1–17  
Journal NCBI Related
117.-Rajewsky, N.,  Almouzni, G.,  Gorski, S.,  .../...,  Marti-Renom, M.A.,  .../... and LifeTime Community
"LifeTime and improving European healthcare through cell-based interceptive medicine"
Nature (2020) 587 377–386  
Journal NCBI Related
116.-Galan, S.,  Machnik, N.,  Kruse, K.,  Díaz, N.,  Marti-Renom, M.A. and Vaquerizas, J.M.
"Quantitative comparison and feature extraction for chromatin contact data using structural similarity"
Nature Genetics (2020) 52 1247–1255  
Journal NCBI Related
115.-Stik, G.,  Vidal, V.,  Barrero, M.,  Cuartero, S.,  Vila-Casadesús, M.,  Mendieta-Esteban, J.,  Tian, T.V.,  Choi, J.,  Berenguer, C.,  le Dily, F.,  Cramer, P.,  Marti-Renom, M.A.,  Stadhouders, R. and Graf, T.
"CTCF is dispensable for cell fate conversion but facilitates acute cellular responses"
Nature Genetics (2020) 52 655–661  
Journal NCBI Related
114.-Farabella, I. and Marti-Renom, M.A.
"TADs without borders"
Nature Genetics (2020) 52 752–753  
Journal NCBI Related
113.-Soler-Vila, P.,  Cusco Pons, P.,  Farabella, I.,  Di Stefano, M. and Marti-Renom, M.A.
"Hierarchical chromatin organization detected by TADpole."
Nucleic Acids Research (2020) 48 (7) e39  
Journal NCBI Related BioRxiv
112.-Di Stefano, M.,  Di Giovanni, F.,  Pozharskaia, V.,  Gomar-Alba, M.,  Baù, D.,  Carey, L.B.,  Marti-Renom, M.A. and Mendoza, M.
"Impact of chromosome fusions on 3D genome organization and gene expression in budding yeast"
Genetics (2020) 214 (3) 651-667  
Journal NCBI Related BioRxiv
111.-Di Stefano, M.,  Stadhouders, R.,  Farabella, I.,  Castillo, D.,  Serra, F.,  Graf, T. and Marti-Renom, M.A.
"Transcriptional activation during cell reprogramming correlates with the formation of 3D open chromatin hubs"
Nature Communications (2020) 11 2564  
Journal NCBI Related BioRxiv
110.-Zhang, N.,  Mendieta-Esteban, J.,  Magli, A.,  Lilja, K.C.,  Perlingeiro, R.C.R.,  Marti-Renom, M.A.,  Tsirigos, A. and Dynlacht, B.D.
"Muscle progenitor specification and myogenic differentiation are associated with changes in chromatin topology"
Nature Communications (2020) 11 6222  
Journal NCBI Related
109.-Serna-Pujol, N.,  Salinas-Pena, M.,  Mugianesi, F.,  Lopez-Anguita, N.,  Torrent-Llagostera, F.,  Izquierdo-Bouldstridge, A.,  Marti-Renom, M.A. and Jordan, A.
"TADs enriched in histone H1.2 strongly overlap with the B compartment, inaccessible chromatin and AT-rich Giemsa bands"
FEBS Journal (2020) 10.1111/febs.15549   
Journal NCBI Related
108.-Nguyen, H.Q.,  Chattoraj, S.,  Castillo, D.,  Nguyen, S.C.,  Nir, G.,  Martins, N.M.C.,  Reginato, P.R.,  Hannan, M.,  Church, G.M.,  Daugharthy, E.R.,  Marti-Renom, M.A. and Wu, C.T.
"3D mapping and accelerated super-resolution imaging of the human genome using in situ sequencing"
Nature Methods (2020) 17 822–832  
Journal NCBI Related
107.-Bogu, G.K.,  Reverter, F.,  Marti-Renom, M.A.,  Snyder, M.P. and Guigó, R.
"Atlas of transcriptionally active transposable elements in human adult tissues"
BioRxiv (2019) preprint   
106.-Codó, L.,  Bayarri, G.,  Cid-Fuentes, J.A.,  Conejero, J.,  Hospital, A.,  Royo, R.,  Repchevsky, D.,  Pasi, M.,  Meletiou, M.,  McDowall, M.D.,  Reham, F.,  Alcantara, J.A.,  Jimenez-Garcia, B.,  Walther, J.,  Illa, R.,  Serra, F.,  Goodstadt, M.,  Castillo, D.,  Sati, S.,  Buitrago, D.,  Brun-Heath, I.,  Fernandez-Recio, J.,  Cavalli, G.,  Marti-Renom, M.A.,  Yates, A.,  Laughton, C.,  Badia, R.M.,  Orozco, M. and Gelpí, J.LL.
"MuGVRE. A virtual research environment for 3D/4D genomics"
BioRxiv (2019) preprint   
105.-Miguel-Escalada, I.,  Bonàs-Guarch, S.,  Cebola, I.,  Ponsa-Cobas, J.,  Mendieta-Esteban, J. ,  Rolando, D.,  Javierre, B.M.,  Atla, G.,  Farabella, I.,  Morgan, C.C.,  García-Hurtado, J.,  Beucher, A.,  Morán, I.,  Pasquali, L.,  Ramos, M.,  Appel, E.V.R.,  Linneberg, L.,  Gjesing, A.P.,  Witte, D.R.,  Pedersen, O.,  Grarup, N.,  Ravassard, P.,  Mercader, J.M.,  Torrents, D.,  Piemonti, L.,   Berney, T.,  de Koning E.,  Kerr-Conte, J.,  Pattou, F.,  Hansen, T.,   Marti-Renom, M.A.,  Fraser, P. and Ferrer, J.
"Human pancreatic islet 3D chromatin architecture provides insights into the genetics of type 2 diabetes"
Nature Genetics (2019) 51 1137–1148  
Journal NCBI Related Fac1000 BioRxiv
104.-Morf, J.,  Wingett, S.W.,  Farabella, I.,  Cairns, J.,   Furlan-Magaril, M.,  Jiménez-García, L.F.,  Liu, X.,  Craig, F.F.,  Walker, S.,  Segons-Pichon, A.,  Andrews, S.,  Marti-Renom, M.A. and Fraser, P.
"RNA proximity sequencing reveals properties of spatial transcriptome organization in the nucleus."
Nature Biotechnology (2019) 37 793–802  
Journal NCBI Related Fac1000 BioRxiv
This article has been highlighted in Nature Methods here.
103.-Vara, C.,  Paytuví-Gallart, A.,  Cuartero, Y.,  Le Dily, F.,  Garcia, F.,  Salvà-Castro, J.,  Gómez-H, L.,  Julià, E.,  Moutinho, C.,  Aiese-Cigliano, R.,  Sanseverino, W.,  Fornas, O.,  Pendàs, A.M.,  Heyn, H.,  Waters, P.D.,  Marti-Renom, M.A. and Ruiz-Herrera, A.
"Three-dimensional genomic structure and cohesin occupancy correlates with transcriptional activity during spermatogenesis."
Cell Reports (2019) 28(2) 352-367  
Journal NCBI Related
102.-Cuadrado, A.,  Giménez-Llorente, D.,  Kojic, A.,  Rodríguez-Corsino, M.,  Cuartero, Y.,  Martín-Serrano, G.,  Gómez-López, G.,  Marti-Renom, M.A. and Losada, A.
"Specific contributions of cohesin-SA1 and cohesin-SA2 to TADs and Polycomb domains in embryonic stem cells."
Cell Reports (2019) 27 3500–3510  
Journal NCBI Related
101.-Spill, Y.G.,  Castillo, D.,  Vidal, E. and Marti-Renom, M.A.
"Binless normalization of Hi-C data provides significant interaction and difference detection independently of resolution."
Nature Communications (2019) 10(1) 1938  
Journal NCBI Related BioRxiv
100.-Pascual-Reguant. L.,  Blanco, E.,  Galan, S.,  Le Dily, F.,  Cuartero, Y.,  Serra-Bardenys, G.,  di Carlo, V.,  Iturbide, A.,  Cebrià-Costa, J.P.,  Nonell, L.,  García de Herreros, A.,  Di Croce, L.,  Marti-Renom, M.A. and Peiró, S.
"Genome-wide mapping of lamin B1 reveals the existence of dynamic and functional euchromatin lamin B1 domains (eLADs) during epithelial-to-mesenchymal transition (EMT)."
Nature Communications (2018) 9(1) 3420  
Journal NCBI Related
99.-Mas, G.,  Blanco, E.,  Ballaré, C.,  Sansó, M.,  Spill, Y.G.,  Hu, D.,  Aoi, Y.,  Le Dily, F.,  Shilatifard, A.,  Marti-Renom, M.A. and Di Croce, L.
"Promoter bivalency favors an open architecture of the stem cell genome"
Nature Genetics (2018) 50 1452–1462  
Journal NCBI Related Fac1000
98.-Stadhouders, R.,  Vidal, E.,  Serra, F.,  Di Stefano, B.,  Le Dily, F.,  Quilez, J.,  Gomez, A.,  Collombet, S.,  Berenguer, C.,  Cuartero, Y.,  Hecht, J.,  Filion, G.,  Beato, M.,  Marti-Renom, M.A. and Graf, T.
"Transcription factors orchestrate dynamic interplay between genome topology and gene regulation during cell reprogramming."
Nature Genetics (2018) 50 238–249  
Journal NCBI Related BioRxiv
97.-Goodstadt, M. and Marti-Renom, M.A.
"Biovisualization of the Genome, from Data Analysis and Hypothesis Generation to Communication and Learning"
Journal of Molecular Biology (2018) 431 1071–1087  
Journal NCBI Related
96.-Kojic, A.,  Cuadrado, A.,  Koninck, A.M.,  Gomez-Lopez, G.,  Rodriguez-Corsino, M.,  Le Dily, F.,  Marti-Renom, M.A. and Losada, A.
"Distinct roles of cohesin-SA1 and cohesin-SA2 in 3D chromosome organization"
Nature Structural and Molecular Biology (2018) 25 496–504  
Journal NCBI Related BioRxiv
95.-Beekman R.,  Chapaprieta V.,  Russiñol, N.,  Vilarrasa-Blasi, R.,   Verdaguer-Dot, N.,  Martens, J.H.A.,  Duran-Ferrer, M.,  Kulis, M.,  Serra, F.,  Javierre,. B.M.,  Wingett, S.W.,  Clot, G.,  Queirós, A.C.,  Castellano, G,  Blanc, J.,  Gut, M.,  Merkel, A.,  Heath, S.,  Vlasova, A.,  Ullrich, S.,  Palumbo, E.,  Enjuanes, A.,   Martín-García, D.,  Beà, S.,  Pinyol, M.,  Aymerich, M.,  Royo, R.,  Puiggros, M.,  Torrents, D.,  Datta, A.,  Lowy, E.,  Kostadima, M.,  Roller, M.,  Clarke, L.,  Flicek, P.,  Agirre, X.,  Prosper, F.,  Baumann, T.,  Delgado, J.,  López-Guillermo, A.,  Fraser, P.,  Yaspo, M-L.,  Guigó, R.,  Siebert, R.,  Marti-Renom, M.A.,  Puente, X.S.,  López-Otín, C.,  Gut, I.,  Stunnenberg, H.G.,  Campo, E. and Martin-Subero, J.I.
"The reference epigenome and regulatory chromatin landscape of chronic lymphocytic leukemia"
Nature Medicine (2018) 24 868–880  
Journal NCBI Related
94.-Nir, G.,  Farabella, I.,  Pérez Estrada, C.,   Ebeling, C.G.,  Beliveau, B.J.,  Sasaki, H.M.,  Lee, S.H.,  Nguyen, S.C.,  McCole, R.B.,  Chattoraj, S.,  Erceg, J.,  Abed, J.A.,  Martins, N.M.C.,   Nguyen, H.Q.,  Hannan, M.A.,  Russell, S.,  Durand, N.C.,  Rao, S.S.P.,  Kishi, J.Y.,  Soler-Vila, P.,  Di Pierro, M.,  Onuchic, J.N.,  Callahan, S.,  Schreiner, J.,  Stuckey, J.,  Yin, P.,  Lieberman Aiden, E.,  Marti-Renom, M.A. and Wu, C.T.
"Walking along chromosomes with super-resolution imaging, contact maps, and integrative modeling"
PLOS Genetics (2018) 14(12) e1007872  
Journal NCBI Related BioRxiv
This article has been highlighted in Nature here.
93.-Vidal, E.,  Le Dily, F.,  Quilez, J.,  Stadhouders, R.,  Cuartero, Y.,  Graf, T.,  Marti-Renom, M.A.,  Beato, M. and Filion, G.
"OneD: increasing reproducibility of Hi-C Samples with abnormal karyotypes"
Nucleic Acids Research (2018) 04 e49  
Journal NCBI Related BioRxiv
92.-Marti-Renom, M.A.,  Almouzni, G.,  Bickmore, W.A.,  Bystricky, K.,  Cavalli, G.,  Fraser, P.,  Gasser, S.M.,  Heard, E.,  Nicodemi, M.,  Orozco, M.,  Pombo, A. and Torres-Padilla, M-E.
"Challenges and guidelines toward 4D nucleome data and model standards"
Nature Genetics (2018) 50 1352–1358  
Journal NCBI Related Fac1000
91.-Trussart, M.,  Yus, E.,  Martinez, S.,  Baù, D.,  Tahara, Y.O.,  Pengo, T.,  Kretschmer, S.,  Swoger, J.,  Miyata, M.,  Marti-Renom, M.A.,  Lluch-Senar, M. and Serrano, L.
"Defined chromosome structure in a genome-reduced bacterium, Mycoplasma pneumoniae."
Nature Communications (2017) 8 14665  
Journal NCBI Related Fac1000
90.-Martínez-Jiménez, F.,  Overington, J.P.,  Al-Lazikani, B. and Marti-Renom, M.A.
"Rational design of non-resistant targeted cancer therapies."
Scientific Reports (2017) 7 46632  
Journal NCBI Related
89.-Quilez, J.,  Vidal, E.,  Le Dily, F.,  Serra, F.,  Cuartero, Y.,  Stadhouders, R.,  Graf, T.,  Marti-Renom, M.A.,  Beato, M. and Filion, G.
"Parallel sequencing lives, or what makes large sequencing projects successful"
GigaSciences (2017) 6 1-6  
Journal NCBI Related BioRxiv
88.-Goodstadt, M. and Marti-Renom, M.A.
"Challenges for visualizing three-dimensional data in genomic browsers"
FEBS Letters (2017) 591 2505–2519   
Journal NCBI Related
87.-Serra, F.,  Baù, D.,  Goodstadt, M.,  Castillo, D.,  Filion, F. and Marti-Renom, M.A.
"Automatic analysis and 3D-modelling of Hi-C data using TADbit reveals structural features of the fly chromatin colors"
PLOS Computational Biology (2017) 13(7) e1005665  
Journal NCBI Related BioRxiv
86.-Cattoni, D.I.,  Cardozo-Gizz, A.M.,  Georgieva, M.,  Di Stefano, M.,  Valeri, A.,  Chamousset, D.,  Houbron, C.,  Dejardin, S.,  Fiche, J-B.,  Marti-Renom, M.A.,  Bantignies, F.,  Cavalli, G. and Nollmann, M.
"Single-cell absolute contact probability detection reveals that chromosomes are organized by modulated stochasticity"
Nature Communications (2017) 8 1753  
Journal NCBI Related BioRxiv
85.-Le Dily, F.,  Serra, F. and Marti-Renom, M.A.
"3D modeling of chromatin structure: is there a way to integrate and reconcile single cell and population experimental data?"
WIREs Comput Mol Sci (2017) e1308  
84.-Baeza-Delgado, C.,  Von Heijne, G.,  Marti-Renom, M.A. and Mingarro, I.
"Biological insertion of computationally designed short transmembrane segments."
Scientific Reports (2016) 6 23397   
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83.-Bogu, G.K.,   Vizan, P.,  Stanton, L.W.,  Beato, M.,  Di Croce, L. and Marti-Renom, M.A.
"Chromatin and RNA maps reveal regulatory long noncoding RNAs in mouse."
Mol Cell Biol (2016) 36 (5) 809-819  
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82.-Martínez-Jiménez, F. and Marti-Renom, M.A.
"Should network biology be used for drug discovery?"
Expert Opinion on Drug Discovery (2016) 10.1080/17460441.201  
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81.-Serra, F.,  Di Stefano, M.,  Spill, Y.G.,  Cuartero, Y.,  Goodstadt, M.,  Baù, D. and Marti-Renom, M.A.
"Restraint-based three-dimensional modeling of genomes and genomic domains"
FEBS Letters (2015) 589 (20) 2987–2995  
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80.-Junier, I.,  Spill, Y.G.,   Marti-Renom, M.A.,  Beato, M. and le Dily, F.
"On the demultiplexing of chromosome capture conformation data"
FEBS Letters (2015) 589 (20) 3005–3013  
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79.-Trussart, M.,  Serra, F.,  Baù, D.,  Junier, I.,  Serrano, L. and Marti-Renom, M.A.
"Assessing the limits of restraint-based 3D modeling of genomes and genomic domains."
Nucleic Acids Research (2015) 43 (7) 3465-3477  
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78.-Sali, A.,  Berman, H.,  Schwede, T.,  Trewhella, J.,  Kleywegt, G.,  Burley, S.,  Markley, J.,  Nakamura, H.,  Adams, P.,  Bonvin, A.,  Chiu, W.,  Dal Peraro, M.,  Di Maio, F.,  Ferrin, T.,  Grünewald, K.,  Gutmanas, A.,  Henderson, R.,  Hummer, G.,  Iwasaki, K.,  Johnson, G.,  Lawson, C.,  Meiler, J.,  Marti-Renom, M.A.,  Montelione, G.,  Nilges, M.,  Nussinov, R.,  Patwardhan, A.,  Rappsilber, J.,  Read, R.,  Saibil, H.,  Schröder, G.,  Schwieters, C.,  Svergun, C.,  Topf, D.,  Ulrich, M.,  Velankar, E. and Westbrook, S.
"Outcome of the First wwPDB Hybrid / Integrative Methods Task Force Workshop"
Structure (2015) 23(7) 1156–1167  
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77.-Belton, J-M.,  Lajoie, B.R.,  Audibert, S.,  Cantaloube, S.,  Lassadi, I.,  Goiffon, I.,  Baù, D.,  Marti-Renom, M.A.,  Bystricky, K. and Dekker, J.
"The conformation of yeast chromosome III is mating type-dependent and controlled by the recombination enhancer."
Cell Reports (2015) 13 1–13  
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76.-Martínez-Jiménez, F. and Marti-Renom, M.A.
"Ligand-target prediction by structural network biology using nAnnoLyze."
PLOS Computational Biology (2015) 11(3) e1004157  
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75.-Rebollo-Lopez, MJ.,  Lelievre, J.,  Alvarez-Gomez, D.,  Castro-Pichel, J.,  Martínez-Jiménez, F.,  Papadatos, G.,  Kumar, V.,  Colmenarejo, G.,  Mugumbate, G.,  Hurle, M.,  Barroso, V.,  Young, R.J.,  Martinez-Hoyos, M.,  Bates, R.H.,  Lopez-Roman, E.M.,  Mendoza-Losana, A.,  Brown, J.R.,  Alvarez-Ruiz, E.,  Marti-Renom, M.A.,  Overington, J.P.,  Cammack, N.,  Ballell, LL. and Barros-Aguire, D.
"Release of 50 new, drug-like compounds and their computational target predictions for open source anti-tubercular drug discovery"
PLOS ONE (2015) 10(12) e0142293  
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74.-Dufour, D. and Marti-Renom, M.A.
"Software for predicting the 3D structure of RNA molecules."
WIREs Comput Mol Sci (2014) 5 (1) 56–61  
73.-Le Dily, F.,  Baù, D.,  Pohl, A.,  Vicent, G.P.,  Serra, F.,  Soronellas, D.,  Castellano, G.,  Wright, R.H.G,  Ballare, C.,  Filion, G.,  Marti-Renom, M.A. and Beato, M.
"Distinct structural transitions of chromatin topological domains correlate with coordinated hormone-induced gene regulation"
Genes & Dev. (2014) 28 2151-2162  
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72.-Martínez-Jiménez, F.,  Papadatos, G.,  Yang, L.,  Wallace, I.M.,  Kumar, V.,  Pieper, U.,  Sali, A.,  Brown, J.R.,  Overington, J.P. and Marti-Renom, M.A.
"Target prediction for an open access set of compounds active against Mycobacterium tuberculosis"
PLOS Computational Biology (2013) 9(10) e1003253  
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71.-Baeza-Delgado, C.,  Marti-Renom, M.A. and Mingarro, I.
"Structure-based statistical analysis of transmembrane segments"
European Biophysics Journal (2013) 42 199-207  
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70.-Köser, C.U.,  Bryant, J.M.,  Becq, J.,  Török, M.E.,  Ellington, M.J.,  Marti-Renom, M.A.,  Carmichael, A.J.,  Parkhill, J.,  Smith, G.P. and Peacock, S.J.
"Whole-genome sequencing for rapid susceptibility testing of M. tuberculosis"
NEJM (2013) 369 290-292  
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This article has been highlighted in Nature here and here.
69.-Kemena, C.,  Bussotti, G.,  Capriotti, E.,  Marti-Renom, M.A. and Notredame, C
"Using tertiary structure for the computation of highly accurate multiple RNA alignments with the SARA-Coffee package"
Bioinformatics (2013) 29 1112-1119  
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68.-López-Pelegrín, M.,  Cerdà-Costa, N.,  Martínez-Jiménez, F.,  Cintas, A.,  Canals, A.,  Peinado, J.R.,  Marti-Renom, M.A.,  López-Otín, C.,   Arolas, J.L. and Gomis-Rüth, F.X.
"A novel family of soluble minimal scaffolds provides structural insight into the catalytic domains of integral-membrane metallopeptidases."
JBC (2013) 288 21279–21294  
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67.-Dekker, J.,  Marti-Renom, M.A. and Mirny, L.A.
"Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data"
Nature Reviews Genetics (2013) 14 390–403  
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66.-Bañó-Polo, M.,  Baeza-Delgado, C.,  Orzáez, M.,  Marti-Renom, M.A.,  Abad, C. and Mingarro, I.
"Polar/Ionizable residues in transmembrane segments: effects on helix-helix packing."
PLoS ONE (2012) 7 e44263  
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65.-Baù, D. and Marti-Renom, M.A.
"Genome structure determination via 3C-based data integration by the Integrative Modeling Platform"
Methods (2012) 58 300–306  
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64.-Marti-Renom, M.A. and Mirny L.
"Bridging the resolution gap in structural modeling of 3D genome organization"
PLoS Computational Biology (2011) 7 e1002125  
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63.-Feuerriegel, I.,  Köser, C.,  Baù, D.,  Rüsch-Gerdes, S.,  Summers, D.,  Archer, J.,  Marti-Renom, M.A. and Niemann, S.
"Impact of fgd1 and ddn diversity in Mycobacterium tuberculosis complex on in vitro susceptibility to PA-824"
Antimicrobial Agents and Chemotherapy (2011) 55 5718-5722  
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62.-Umbarger, M.A.,  Toro, E.,  Wright, M.A.,  Porreca, G.J.,  Baù, D.,  Hong, S-H.,  Fero, M.J.,  Zhu, J.,  Marti-Renom, M.A.,  McAdams, J.H.,  Shapiro, L.,  Dekker, J. and Church, G.M.
"The three-dimensional architecture of a bacterial genome and Its alteration by genetic perturbation"
Molecular Cell (2011) 44 252–264  
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This article has been highlighted in a Journal Club at the NRMCB and in a News & Views at NRM.
61.-Martínez-Gil, L. ,  Saurí, A.,  Marti-Renom, M.A. and Mingarro, I
"Membrane protein integration into the ER"
FEBS Journal (2011) 278 3846–3858  
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60.-Capriotti, E.,  Norambuena, T,  Marti-Renom, M.A. and Melo, F.
"All-atom knowledge-based potential for RNA structure prediction and assessment"
Bioinformatics (2011) 27 1086-1093  
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59.-Sanyal, A.,  Baù, D.,  Marti-Renom, M.A. and Dekker, J.
"Chromatin globules: a common motif of higher-order chromosome structure?"
Current Opinion in Cell Biology (2011) 23 325–33  
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58.-Bañó-Polo, M. ,  Baldin, F.,  Tamborero, S.,  Marti-Renom, M.A. and Mingarro, I
"N-Glycosylation efficiency is determined by the distance to the C-terminus and the amino acid preceding an Asn-Ser-Thr sequon."
Protein Science (2011) 20 179–186  
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57.-Baù, D. and Marti-Renom, M.A.
"Structure determination of genomic domains by satisfaction of spatial restraints"
Chromosome Research (2011) 19 (1) 25  
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56.-Baù, D.,  Sanyal, A.,  Lajoie, B.R.,  Capriotti, E.,   Byron, M.,   Lawrence J.B.,  Dekker, J. and Marti-Renom, M.A.
"The three-dimensional folding of the α-globin gene domain reveals formation of chromatin globules"
Nature Structural and Molecular Biology (2011) 18 107-114  
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This article has been highlighted in a Technology Feature at the Nature Journal.
55.-Capriotti, E. and Marti-Renom, M.A.
"Quantifying the relationship between sequence and three-dimensional structure conservation in RNA"
BMC Bioinformatics (2010) 11 322  
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54.-Madhusudhan, MS.,  Webb, B.,  Marti-Renom, M.A.,  Eswar, N. and  Sali, A.
"Alignment of multiple protein structures based on sequence and structure features."
PEDS (2009) 22 569-574   
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53.-Capriotti, E. and Marti-Renom, M.A.
"SARA: a server for function annotation of RNA structures"
Nucleic Acids Research (2009) 37 W260-5  
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52.-Fornes, O.,  Aragues, R.,  Espadaler, J.,  Marti-Renom, M.A.,  Sali, A. and Oliva, B.
"ModLink+: Improving fold recognition by using protein-protein interactions"
Bioinformatics (2009) 25 1506-12  
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51.-Orti, L.,   Carbajo, R.J.,   Pieper, U.,  Eswar, N.,  Maurer, S.M.,  Rai, A.K.,  Taylor, G.,  Todd, M.H.,  Pineda-Lucena, A.,  Sali, A. and Marti-Renom, M.A.
"A kernel for open source drug discovery in tropical diseases"
PLoS Neglected Tropical Diseases (2009) 3 e18  
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50.-Orti, L.,   Carbajo, R.J.,   Pieper, U.,  Eswar, N.,  Maurer, S.M.,  Rai, A.K.,  Taylor, G.,  Todd, M.H.,  Pineda-Lucena, A.,  Sali, A. and Marti-Renom, M.A.
"A kernel for the Tropical Disease Initiative"
Nature Biotechnology (2009) 27 320-321  
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49.-Pieper, U.,  Eswar, N.,  Webb, B.M.,  Eramian, D.,  Kelly, L.,  Barkan, D.T.,  Carter, H.,  Mankoo, P.,  Karchin, R.,  Marti-Renom, M.A.,  Davis, F.P. and Sali, A.
"MODBASE, a database of annotated comparative protein structure models, and associated resources."
Nucleic Acids Research (2009) 37 D347-D354  
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48.-Espadaler, J.,  Eswar, N.,  Querol, E.,  Aviles, F.X.,  Sali, A.,  Marti-Renom, M.A. and Oliva, B.
"Prediction of enzyme function by combining sequence similarity and protein interactions"
BMC Bioinformatics (2008) 9(1) 249  
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47.-Panjkovich, A.,  Melo, F. and Marti-Renom, M.A.
"Evolutionary potentials: structure specific knowledge-based potentials exploiting the evolutionary record of sequence homologs"
Genome Biology (2008) 9 R68  
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46.-Capriotti, E. and Marti-Renom, M.A.
"Computational RNA structure prediction "
Current Bioinformatics (2008) 3 (1) 32-45  
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45.-Capriotti, E.,  Arbiza, L.,  Casadio, R.,  Dopazo, J.,  Dopazo, H. and Marti-Renom, M.A.
"The use of estimated evolutionary strength at the codon level improves the prediction of disease related protein mutations in human."
Human Mutation (2008) 29 (1) 198-204  
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44.-Capriotti, E. and Marti-Renom, M.A.
"RNA structure alignment by a unit-vector approach"
Bioinformatics (2008) 24 i112-i118  
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43.-Eswar, N.,  Webb, B.,  Marti-Renom, M.A. ,  Madhusudhan, M.S.,  Eramian, D.,  Shen, M-Y.,  Pieper, U. and Sali A.
"Comparative Protein Structure Modeling Using MODELLER. "
Current Protocols in Protein Science (2007) 2.9 (Nov 2007) 2.9.1-2.9.31  
Journal NCBI Related pdf This is an updated and revised version of the CPPS unit published in Nov. 2002
42.-Marti-Renom, M.A.,   Rossi, A.,  Al-Shahrour, F.,   Davis, F.,  Pieper, U.,  Dopazo, J. and Sali, A.
"The AnnoLite and AnnoLyze programs for comparative annotation of protein structures"
BMC Bioinformatics (2007) 8 (Suppl 4) S4  
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41.-Stanley, W.A.,  Fodor, K.,   Marti-Renom, M.A.,  Schliebs, W. and Wilmanns, M.
"Protein translocation into peroxisomes by ring-shaped import receptors"
FEBS Letters (2007) 581 4795-802  
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40.-Marti-Renom, M.A.,  Pieper, U.,  Madhusudhan, M.S.,  Rossi, A.,  Eswar, N.,  Davis, F.P.,  Al-Shahrour, F.,  Dopazo, J. and  Sali A.
"DBAli tools: mining the protein structure space"
Nucleic Acids Research (2007) 35 W393-W397  
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39.-Aragues, R.,   Sali, A.,  Bonet, J.,  Marti-Renom, M.A. and Oliva, B.
"Characterization of protein hubs by inferring interacting motifs from protein interactions"
PLoS Computational Biology (2007) 3(9) e178  
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38.-Melo, F. and Marti-Renom, M.A.
"Accuracy of sequence alignment and fold assessment using reduced amino acid alphabets"
Proteins (2006) 63 986-995  
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37.-Kepler, T.,  Marti-Renom, M.A.,  Maurer, S.M.,  Rai A.K.,  Taylor, G. and Todd, M.H
"Open Source Research - The power of Us"
Aust. J. Chem. (2006) 59 291-294  
36.-Eswar, N.,  Webb, B.,  Marti-Renom, M.A. ,  Madhusudhan, M.S.,  Eramian, D.,  Shen, M-Y.,  Pieper, U. and Sali A.
"Comparative Protein Structure Modeling with MODELLER"
Current Protocols in Bioinformatics (2006) 5.6 (Dec 2006) 5.6.1-5.6.30  
Journal NCBI Related pdf This is an updated and revised version of the CPBI unit published in Nov 2003
35.-Topf, M.,  Baker, ML.,  Marti-Renom, MA.,  Chiu, W and Sali, A
"Structure characterization of assembly components by iterative comparative modeling and cryoEM density fitting"
J. Mol. Biol. (2006) 357(5) 1655-68  
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34.-Pieper, U.,  Eswar, N.,   Davis, F.,   Braberg, H.,  Madhusudhan, M.S.,,  Rossi, A.,  Marti-Renom, M.A.,  Karchin, R.,  Webb, B.,  Eramian, D.,  Shen, M-Y.,  Kelly, L.,  Melo, F. and Sali, A.
"MODBASE, a database of annotated comparative protein structure models, and associated resources"
Nucleic Acids Research (2006) 34 D291-295  
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33.-Madhusudhan, MS.,  Marti-Renom, MA.,  Sanchez, R. and Sali, A.
"Variable gap penalty for protein sequence-structure alignment"
PEDS (2006) 19 129-133  
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32.-Rossi, A.,  Marti-Renom, M.A. and Sali, A.
"Localization of binding sites in protein structures by optimization of a composite scoring function"
Protein Science (2006) 15 2366-2380  
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31.-Eramian, D.,  Shen, M-Y.,  Devos, D.,  Melo, F.,  Sali, A. and Marti-Renom, M.A.
"A composite score for predicting errors in protein structure models"
Protein Science (2006) 15 1653-1666  
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30.-McMahon, S.A.,  Miller, J.L.,  Lawton, J.A.,  Kerkow, D.E.,  Hodes, A.,  Marti-Renom, M.A.,  Doulatov, S.,  Eswar, N.,  Sali, A.,  Miller, J.F. and Ghosh, P.
"The C-type lectin fold as a scaffold for massive sequence variation"
Nature Structural and Molecular Biology (2005) 12 886-892  
Journal NCBI Related Fac1000 recommended
29.-Espadaler, J.,  Aragues, R.,  Eswar, N.,  Marti-Renom, M.A.,  Querol, E.,  Aviles, F.X.,  Sali, A. and Oliva, B.
"Detecting remote homology by sequence similarity and protein-protein interactions."
Proc. Natl. Acad. Sci. USA. (2005) 102 7151-7156  
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28.-Mirkovic, N.,  Marti-Renom, M.A.,  Weber, B.L.,  Sali, A. and Monteiro, A.N.A.
"Structure-based assessment of missence mutations in human BRCA1: Implications for breast and ovarian cancer predisposition."
Cancer Research (2004) 64 3790-3797  
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27.-Pieper, U.,  Eswar, N.,  Braberg, H.,  Madhusudhan, MS.,  Davis, FP.,  Stuart, AC.,  Mirkovic, N.,  Rossi, A.,  Marti-Renom, MA.,  Fiser, A.,  Webb, B.,  Greenblatt, D.,  Huang, CC.,  Ferrin, TE. and Sali, A.
"MODBASE, a database of annotated comparative protein structure models, and associated resources."
Nucleic Acids Res (2004) 32 D217-22  
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26.-Marti-Renom, M.A.,  Madhusudhan, M.S. and Sali, A.
"Alignment of protein sequences by their profiles"
Protein Science (2004) 13 1071-1087  
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25.-Marti-Renom, M.A.,   Fiser, A.,  Madhusudhan, M.S.,  John, B.,  Stuart, A.,  Eswar, N.,  Pieper, P.,  Shen, MY. and Sali, A.
"Modeling protein structure from its sequence"
Current Protocols in Bioinformatics. Ed: John Wiley & Sons, Inc. (2003) 5.1 (Nov 2003) 5.1.1-5.1.22  
Journal pdf This is an updated and revised version of the original CPBI unit published in Jan 2003
24.-Marti-Renom, M.A.
"Protein Structure Modeling for Structural Genomics"
Business Briefing: Future Drug Discovery (2003) June 59-63  
Journal pdf
23.-Marti-Renom, M.A.,  Yercovich, B. and Sali, A.
"Modeling protein structure from its sequence."
Current Protocols in Bioinformatics. Ed: John Wiley & Sons, Inc. (2003) 5.1 (Jan 2003) 5.1.1-5.1.22  
Journal pdf
22.-Koh, I-Y. Y. ,  Eyrich, V.A.,  Marti-Renom, M.A.,  Przybylski, D.,  Madhusudhan, M.S.,  Narayanan, E.,  Graña, O.,  Pazos, F.,  Valencia, A.,  Sali, A. and Rost, B.
"EVA: evaluation of protein structure prediction servers"
Nucleic Acids Research (2003) 31 3311-3315  
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21.-Narayanan, E.,  John, B.,  Mirkovic, N.,  Fiser, A.,  Ilyin, V.,  Pieper, U.,  Stuart, A.C.,  Marti-Renom, M.A.,  Madhusudhan, M.S.,  Yerkovich, B. and Sali A.
"Tools for comparative protein structure modeling and analysis"
Nucleic Acids Research (2003) 31 3375-3380.  
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20.-Ilyin, VA.,  Pieper, U.,  Stuart, AC.,  Marti-Renom, MA.,  McMahan, L. and Sali, A.
"ModView, visualization of multiple protein sequences and structures."
Bioinformatics (2003) 19 165-6  
home journal MedLine related pdf
19.-Iverson, GM.,  Reddel, S.,  Victoria, EJ.,  Cockerill, KA.,  Wang, YX.,  Marti-Renom, MA.,  Sali, A.,  Marquis, DM.,  Krilis, SA. and Linnik, MD.
"Use of Single Point Mutations in Domain I of beta(2)-Glycoprotein I to Determine Fine Antigenic Specificity of Antiphospholipid Autoantibodies."
J Immunol (2002) 169 7097-7103  
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18.-Martí-Renom, M.A.,  Madhusudhan, M.S.,  Fiser, A.,  Rost, B. and Sali, A.
"Reliability of assessment of protein structure prediction methods"
Structure (2002) 10 435--440  
journal NCBI Related pdf Fac1000 recommended
17.-Sali, A.,  Martí-Renom, M.A.,  Madhusudhan, M.S.,  Fiser, A. and Rost, B.
"Reply To Moult et al."
Structure (2002) 10 292--293  
Journal pdf
16.-Martí-Renom, M.A.,  Yercovich, B. and Sali, A.
"Comparative Protein Structure Prediction"
Current Protocols in Protein Science (2002) 1 2.9.1-2.9.22,  
Journal pdf
15.-Eyrich, V.,  Martí-Renom, M.A.,  Przybylski, D.,  Fiser, A.,  Madhusudhan, M.S.,  Pazos, F.,  Valencia, A.,  Sali, A. and Rost, B.
"EVA: continuous automatic evaluation of protein structure prediction servers."
Bioinformatics (2001) 17 1242-1243  
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14.-Marti-Renom, MA.,  Ilyin, VA. and Sali, A.
"DBAli: a database of protein structure alignments."
Bioinformatics (2001) 17 746-7  
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13.-Mas, JM.,  Aloy, P.,   Martí-Renom, M.A.,  Oliva, B.,  de Llorens, R.,  Aviles, FX. and Querol, E.
"Classification of protein disulphide-bridge topologies."
J Comput Aided Mol Des (2001) 15 477-87  
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12.-Sánchez, R.,  Pieper, U.,  Melo, F.,  Eswar, N.,  Martí-Renom, M.A.,  Madhusudhan, M.S.,  Mirkovic, N. and Sali, A.
"Protein structure modeling for structural genomics"
Nat Struct Biol (2000) 7 Suppl 986--90  
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11.-Martí-Renom, M.A.,  Stote, R.H.,  Querol, E.,  Avilés, F.X. and Karplus, M.
"Structures of scrambled disulfide forms of the potato carboxypeptidase inhibitor predicted by molecular dynamics simulations with constraints."
Proteins (2000) 40 482--493  
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10.-Martí-Renom, M.A.,  Stuart, A.,  Fiser, A.,  Sánchez, R.,  Melo, F. and Sali, A.
"Comparative protein structure modeling of genes and genomes."
Annu Rev Biophys Biomol Struct (2000) 29 291--325  
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9.-Serra-Hartmann, X.,  Rebordosa, X.,  Piñol, J.,  Querol, E. and Martí-Renom, M.A.
"ASAP analysis of peptide composition."
Bioinformatics (2000) 16 1153--1154  
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8.-Aloy, P.,  Mas, J.M.,  Martí-Renom, M.A.,  Querol, E.,  Avilés, F.X. and Oliva, B.
"Refinement of modelled structures by knowledge-based energy profiles and secondary structure prediction: application to the human procarboxypeptidase A2."
J Comput Aided Mol Des (2000) 14 83--92  
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7.-Liedtke, W.,  Choe, Y.,  Martí-Renom, M.A.,  Bell, A.M.,  Denis, C.S.,  Sali, A.,  Hudspeth, A.J.,  Friedman, J.M. and Heller, S.
"Vanilloid receptor-related osmotically activated channel (VR-OAC), a candidate vertebrate osmoreceptor"
Cell (2000) 103 525--35  
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6.-Martí-Renom, M.A.
"ASAP, web server for analysis of peptide composition"
CCP11 Newsletters (1999) 9 2-3  
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5.-Martí-Renom, M.A.,  Stote, R.H.,  Querol, E.,  Avilés, F.X. and Karplus, M.
"Refolding of potato carboxypeptidase inhibitor by molecular dynamics simulations with disulfide bond constraints"
J Mol Biol (1998) 284 145--72  
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4.-Mas, J.M.,  Aloy, P.,  Martí-Renom, M.A.,  Oliva, B.,  Blanco-Aparicio, C.,  Molina, M.A.,  de, Llorens, R.,  Querol, E. and Avilés, F.X.
"Protein similarities beyond disulphide bridge topology"
J Mol Biol (1998) 284 541--8  
Journal NCBI Related pdf
3.-Stote ,R.H.,  Martí-Renom, M.A.,  Querol, E.,  Aviles, F.X. and Karplus, M.
"Molecular dynamics simulations of the unfolding and refolding of potato carboxypeptidase inhibitor"
ABSTR PAP AM CHEM S (1998) 216 U272  
2.-Martí-Renom, M.A.,  Mas, J.M.,  Aloy, P.,  Querol, E.,  Avilés, F.X. and Oliva, B.
"Statistical Analysis of the Loop-geometry on a Non-redundant Database of Proteins"
J Mol Model (1998) 11 347--354  
journal pdf
1.-Martí-Renom, M.A.,  Mas, J.M.,  Oliva, B.,  Querol, E. and Avilés, F.X.
"Effects of counter-ions and volume on the simulated dynamics of solvated proteins. Application to the activation domain of procarboxypeptidase B"
Protein Eng (1998) 11 881--90  
Journal NCBI Related pdf

There are 11 publications of book type

11.-Marti-Renom, M.A.
"Nucleoma 4D"
(2022) Observatorio de Tendencias Madrid, Spain   
10.-Di Stefano, M.,  Castillo, D.,  Serra, F.,  Farabella, I.,  Goodstadt, M. and Marti-Renom, M.A.
"Analysis, Modeling, and Visualization of Chromosome Conformation Capture Experiments."
(2021) Humana New York, NY 35-63  
9.-Di Stefano, M. and  Marti-Renom, M.A.
"Restraint-based modeling of genomes and genomic domains"
(2019) CRC Press 233  
8.-Di Stefano, M.,  Castillo, D.,  Serra, F.,  Farabella, I.,   Goodstadt, M. and Marti-Renom, M.A.
"Analysis, modeling and visualization of Chromosome Conformation Capture experiments"
(2019) Springer   
7.-Dufour, D. and Marti-Renom, M.A.
"Modeling of RNA sequences"
(2013) Springer Edition 2013 p1566-1569  
Journal Amazon
6.-Dufour, D.,  Capriotti, E. and Marti-Renom, M.A.
"Computational methods for RNA structure prediction and analysis."
(2013) PanStanford Publishing 1st edition   
5.-Marti-Renom, M.A.,  Capriotti, E.,  Shindyalov, I. and Bourne, P.
"Structural Comparison and Alignment. In: Structural Bioinformatics. "
(2009) Wiley-Blackwell, New Jersey. USA. 2nd Edition   
4.-Engelen, S. and Marti-Renom, M.A.
"Open source drug discovery: The Tropical Disease Initiative. In: In Sickness and in Health. The Future of Medicine: Added Value and Global Access."
(2009) VUBPRESS, Brussels, Belgium   
3.-Capriotti, E. and Marti-Renom, M.A.
"Assessment of protein structure predictions. In: Computational Structural Biology. "
(2008) World Scientific Publishing Company. New Jersey. USA.   
2.-Madhusudhan, M.S.,  Marti-Renom, M.A.,   Eswar, N.,  John, B,  Pieper, U.,   Karchin, R.,  Shen, M-Y and Sali, A
"Comparative protein structure prediction. In: The Proteomics Protocols Handbook."
(2005) Humana Press Inc. Totowa, NJ. 835-864  
Journal Amazon
1.-Barbadilla, A.,  Naveira, H.,  Santos, M.,  Martí-Renom, M.A. and Peris, F.
"Introducción al BMDP en VAX/VMS"
(1992) UAB, Bellaterra, Spain   
Practices book for Biostatistics at 3rd grade in Biology studies

There are 11 publications of phdthesis type

11.-Mugianesi, F.,  Di Croce, L. and Marti-Renom, M.A.
"The role of chromatin-associated factors in genome topology"
(2022) Barcelona, Spain   
10.-Sparavier, A.,  Di Croce, L. and Marti-Renom, M.A.
"Creating the AML-specific t(9;11) chromosomal translocation model to study the structural basis of leukemia development in mouse cells"
(2022) Barcelona, Spain   
9.-Mendieta-Esteban, J.,  Farabella, I. and Marti-Renom, M.A.
"Chromatin 3D modelling from sparse 3C- based datasets"
(2020) Barcelona, Spain   
8.-Galan, S.,  Serra, F. and Marti-Renom, M.A.
"Chromatin organization: Meta-analysis for the identification and classification of structural patterns"
(2020) Barcelona, Spain   
7.-Soler-Vila, P. and Marti-Renom, M.A.
"Mulsti-scale study of the genome architecture and its dynamical facets"
(2019) Barcelona, Spain   
6.-Baeza-Delgado, C.,  Marti-Renom, M.A. and Mingarro, I.
"On the design of optimally inserted transmembrane helices"
(2017) Valencia, Spain   
5.-Bogu, G.K.,  Marti-Renom, M.A. and Guigó, R.
"Understanding the transcriptional landscape of non-coding genome (lncRNAs and repetitive elements) in mammals"
(2017) Barcelona, Spain   
4.-di Giovanni, F.,  Marti-Renom, M.A. and Mendoza, M.
"The impact of chromosome positioning in nuclear functions"
(2016) Barcelona, Spain   
3.-Martínez-Jiménez, F. and Marti-Renom, M.A.
"Structural study of the therapeutic potential of protein-ligand interactions"
(2016) Barcelona, Spain   
2.-Trussart, M.,  Marti-Renom, M.A. and Serrano, L.
"Structure determination of Mycoplasma pneumoniae genome"
(2015) Barcelona, Spain   
1.-Martí-Renom, M.A.
"On the Unfolding and Refolding of Potato Carboxypeptidase Inhibitor"
(1999) Bellaterra, Spain   
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